Molecular Epidemiology of Pathogens

Question 1

What features should variables we test consist of

Answer 1

• Reliable
• Repeatable
• Reproducible

Question 2

What is molecular epidemiology

Answer 2

A resolved measure of differences that determines:

• Disease distribution in time and place
• Disease transmission
• Disease manifestation
• Disease progression

Question 3

What main questions does molecular epidemiology answer

Answer 3

• Confirming outbreaks
• Identifying disease risk

Question 4

How can we use information from confirming outbreaks

Answer 4

inside institutions:

• Did patient A catch this pathogen from patient B?
• Do patients A, B & C from the same hospital ward have the same strain?

in the community:

• Who was the index case and what is the likely source?

in the past:

• What has driven the geographical spread of important strains?

in the lab:

• Is this an outbreak or a contaminant?

Question 5

What can we target to examine

Answer 5

• Functional characteristics
• Genomic characteristics

Question 6

Give some examples of functional characteristics that we may look for

Answer 6

• Classical - Biochemistry
• Serology - O157 antigen
• Virulence - Verotoxin

Question 7

Give examples of genomic characteristics that we may look for

Answer 7

• DNA - Gene, amino acid seq, base seq
• RNA - Ribosome, miRNA

Question 8

How much diversity should a factor of interest have

Answer 8

• Single weighting - presence or absence
• Additive weighing - Combination of single tests
• Multiple weighting - Genomic factors

Question 9

What subsets can we look for in genomic factors

Answer 9

• Factoral - presence or absence of a gene
• Functional - Type of substitution
• Temporal - Mutation rate

Question 10

How does factorial multiple copy number systems work

Answer 10

• PCR with RE region primers generates multiple lengths amplicons
• Hybridisation of labelled PCR products onto 43 specific oligonucleotides
• Fixed on a membrane then visualise signal with RE probe

Question 11

How can we test for functional diversity

Answer 11

• Single base substitutions can cause changes in DNA sequence, creating different possibilities and relations between each sequence present
• Synonymous, non-synonymous and corruptive mutations can change the function output of the sequence

Question 12

How can we measure mutation rate

Answer 12

• There is a constant molecular clock where we can expect a change to occur after that time limit

Question 13

What factors affect the molecular clock

Answer 13

• Bacterial replication rate
• Proof reading fidelity
• Selection pressure from host/environment
• Degree of redundancy
• Transmission rate

Question 14

What genes can change the most

Answer 14

• Hyper-variable genes change more rapidly than conserved genes
• Conserved genes are more likely to be associated with phenotype and virulence
• Not all changes are new
  Some may revert to an older profile (convergent evolution)
• Large and rapid changes are rare but often lead to escape from existing herd protection

Question 15

Give examples of epidemiological associations

Answer 15

• Transmission - Hospital-acquired infection
• Reservoirs of infection - Contact tracing, Determining introduction events
• Spread or emergence of resistance